The goal of this project is to provide additional data and statistical analyses for differentiating between prehistoric/historic Native American remains and modern forensic cases that may be potentially confusing. Forensic anthropologists often receive requests from local law enforcement to infer whether skeletal remains are of forensic or non-forensic significance. Skeletal remains of non-forensic significance are commonly of Native American ancestry, but the empirical methods common for determining Native American affinity from skeletal remains have not been established for California prehistoric/historic Native Americans. Therefore, forensic anthropologists working in California lack empirical methods for not only identifying prehistoric California Native American remains, but also differentiating them from modern/forensic populations whose skeletal attributes are similar. In particular, skeletal remains of Latin American US immigrants of indigenous origins are becoming more present in the forensic anthropological laboratory, and can exhibit the same suite of skeletal traits classically used to identify Native American affinity. In this article, we initiate an investigation into this issue by analyzing both craniometric and morphoscopic data using a range of statistical methods for differentiating prehistoric Northern California Native Americans from modern Guatemalan Maya. Our discriminant analyses results indicate that by using nine craniometric variables, group classification is 87% correct. In addition, seven morphoscopic variables can predict group classification correctly for 77% of the sample. The results suggest that it is possible to differentiate between our two samples. Such a method contributes to the efficient and empirical determination of temporal and geographic affinity, allowing for the repartriation of Native American remains to their tribes, as well as the accurate analysis of forensically significant remains. Copyright © 2010 John Wiley & Sons, Ltd.